The PADI referral is for when a split course is taking place, for example if INS/Company "X" teaches a customer the classroom portion (or any part of a course) but then passes the student onto another INS/Company "Y" to complete the course. It is quite common for a Student to do classroom and pool with one company and then through a referral to do open water exercise portion with another INS/company.
There is also a local referral deal that operates between dive operations, for example if you are a PADI "pro" you should be able to get 10/20% of the course fee as "referral fee" for handing over the student to another instructor/company. Wierd thing is (esp. Pattaya!) that you cannot, as a customer, get this 10/20% discounted by going direct - through the refferrer or the the final training company, you still pay exactly the same fee - go figure!
Same goes for booking boats - although strangely - its actually much much cheaper to book a days diving through a referrer than to go directly to company running the boat - I have personally paid between 1200 Baht and 3000 Baht for a days diving on the same boat but booked through different referrers. Booking a day in Pattaya with an operator in Bangkok is nearly allways the cheapest way to dive in Pattaya. Surprisingly the the Pattaya operations have a little group called PASS (Pattaya Alliance for Safe Scuba) who's main task seems to be enforcing a price fixing cartel amongst Pattaya operators - they usually want upto 3000 Baht a day (with equipment)!!
I find the pricing on Koh Tao much more acceptable as they do seem to be at each others throats regarding prices and even if they price fix also its not such a problem because you can get transfer from Samui to Tao, diving, accomodation, equipment, and transfer back to Samui plus nicer diving! for less than it would cost you for a weekend in Pattaya. I did it with SIDS on Samui they offered a great package on Tao for about 6000 Baht.
One last thing - if you want to buy equipment tell your instructor what you wnat and that you will give him 10% for going in the shop and buying it for you - as he normally gets 30% discount you can both get a deal.
Happy Xmas